tbuckley/cabot-search huggingface dataset:
DIPG-33. P16 IMMUNOHISTOCHEMICAL EXPRESSION AS A SURROGATE ASSESSMENT OF CDKN2A ALTERATION IN GLIOMAS LEADING TO PROGNOSTIC SIGNIFICANCES
Authors: Lucas Geyer, Thibaut Wolf, Marie Pierre Chenard, Helene Cebula, Roland Schott, Georges Noel, Eric Guerin, Erwan Pencreach, Damien Reita, Natacha ENTZ-WERLE, Benoit Lhermitte
Journal: Neuro-Oncology (2023)

Abstract CDKN2A is a tumor suppressor gene encoding for p16 protein. Its homozygous deletion is a central prognostic factor for numerous brain cancers. This deletion can be detected by several techniques. Up to now, immunohistochemistry (IHC) using p16 antibody is not recommended as a surrogate test. This study aimed to evaluate to what extent IHC levels of p16 expression may provide information about CDKN2A homozygous deletion. A retrospective study was conducted in 173 gliomas comprising 50 circumscribed low-grade MAPK-altered gliomas, 18 pediatric diffuse high-grade gliomas (HGG), and 105 adult-type diffuse gliomas of all grade, using p16 IHC and CDKN2A fluorescent in situ hybridization. Survival analyses were performed to assess their prognostic impact. Three patterns of p16 expression were observed: absence of expression, focal expression and overexpression. The prognostic impact of p16 overexpression was dependent on the tumor drivers. Indeed, it was associated to a better prognosis in MAPK-induced tumors, but to a worse survival in IDH-wild-type glioblastomas. CDKN2A homozygous deletion present in all type of high grade pediatric or adult gliomas was significantly linked to a worse outcome in the entire population. Regarding specifically to H3K27-altered gliomas, no significant prognostic impact was observed, probably related to the small size of our population. Nevertheless, this p16 lost expression was rarely reported in this pediatric population. The lost expression was observed in 7/9 H3K27M-mutants and in 6/8 wild-type cases. Its implication should be considered more largely and is probably opening the path for therapies targeting the p16 pathway in this population. Regarding the IHC technique itself, beyond the association between absence of p16 protein expression and the CDKN2A loss (p&amp;lt;0.001), this technique seems to have a strong sensitivity and a high negative predictive value. These data suggest that p16 IHC might be a pertinent test to detect cases harboring CDKN2A homozygous deletion.
HGG-17. SINGLE-CELL AND SPATIAL ANALYSES DECIPHER THE UNIQUE INVASIVE GROWTH PATTERN OF GLIOMATOSIS CEREBRI
Authors: Shauna Crampsie, Ilon Liu, Lucia Lisa Petrilli, Alan Mackay, Giulio Spinozzi, Yura Grabovska, Olivia A Hack, Ketty Kessler, Sara Temelso, Diana Martins Carvalho, Anna Burford, Drenusha Sejdiu, Valeria Molinari, McKenzie L Shaw, Hafsa M Mire, Giulia Pericoli, Alfredo Cerimele, Clémentine Barry, Carolina Cocito, Marie-Anne Debily, Thomas Kergrohen, Yassine Ajlil, Kévin Beccaria, Pascale Varlet, Arnault Tauziède-Espariat, Angela Mastronuzzi, Andrea Carai, Isabella Giovannoni, Sabrina Rossi, Evelina Miele, Jacques Grill, Thomas S Jacques, Jeffery P Greenfield, David Castel, Maria Vinci, Mariella G Filbin, Chris Jones
Journal: Neuro-Oncology (2023)

Abstract Gliomatosis cerebri (GC) is a rare, lethal glioma that is radiologically diagnosed and characterised by its diffuse infiltration throughout the cerebral lobes of the brain. It is no longer recognised as a separate entity by the WHO classification, but its growth pattern and invasive phenotype differ from other types of glioma. In order to understand what underlies this unique presentation, we sought to unravel these complex tumours in children through single cell and spatial approaches. 26 paediatric cases (1.3-19 years, median=11.3) were collected for DNA methylation, whole exome sequencing and single cell RNA-sequencing. Of these, 16 cases were used for Imaging Mass Cytometry (IMC). 5 patient-derived cell lines were used to model migration and invasion in vitro, whereby we have also been able to explore gene expression differences associated with the invading cells by RNAseq. We analyzed the transcriptional landscape of all 26 GC patients at single-cell resolution, and identified shared tumor cellular programs of glial and neuronal lineage. We observed notable heterogeneity of neuronal lineage tumor cells that were composed of different states, such as metabolic active and synaptogenic states. We described tumor cell states associated with higher invasivity, as corroborated from integrated analysis with our in vitro invasion-associated gene expression profiles. Next, we stratified all tumors by their DNA methylation profiles, and defined 16 archetypal GC cases, for which we show specific transcriptional features. Furthermore, we analyzed multiple regions of interest within FFPE patient tissue sections by IMC and demonstrate spatial patterns in the interaction between the tumour and normal brain tissue interface, and inter-regional heterogeneity for stem, invasive and proliferative markers. Together, we dissect the characteristic invasive phenotype of GC at multiple molecular, spatial and functional layers, thereby providing the basis for modelling and therapeutic avenues much needed for this lethal disease.
HGG-02. METABOLIC TARGETING OF HIGH-GRADE GLIOMAS WITH MTAP LOSS
Authors: Bavani Subramaniam, Bettina Kritzer, Ethan Putnam, Gary Cunningham, Surajit Bhattacharya, Roger Packer, Miriam Bornhorst, Javad Nazarian
Journal: Neuro-Oncology (2023)

Abstract Malignant transformation of pediatric glioma is often associated with homozygous deletion of CDKN2A. With CDKN2A loss, MTAP which is in the same chromosomal location, 9p21, is homozygously deleted in a majority of HGGs and some LGGs. The MTAP gene codes for methylthioadenosine phosphorylase (MTAP) protein which plays an important role in methionine salvage pathway. Absence of MTAP results in accumulation of 5’-methylthioadenosine (MTA), de novo purine synthesis, and tumor cell dependency on protein arginine methyltransferase 5 (PRMT5) and its substrate provider, methionine adenosyltransferase II alpha (MAT2A). We hypothesize that drugs targeting PRMT5, MAT2A, and de novo purine synthesis, in combination with drugs targeting hyper-activated RAS/MAPK pathway, will be effective in inhibiting MTAP-null glioma growth. Patient-derived glioma cells were validated for MTAP loss using genome sequencing, RNA sequencing and western blot. MTA accumulation caused by MTAP loss was validated through high-performance liquid chromatography. Cells were subjected to monotherapy and combination drug therapy with PRMT5, MAT2A and de novo purine synthesis inhibitors, in addition to drugs targeting RAS/MAPK signaling pathway. Additionally, MTAP-null (MTAPnull) in vivo models are being developed.We show accumulation of MTA in MTAPnull cells compared to MTAP-wild type (MTAPWT) cells, caused by loss of MTAP that cleaves MTA to adenine and 5-methylthioribose-1-phosphate (MTR). Accumulation of MTA makes MTAPnull glioma cells more sensitive to MAT2A inhibitor AG-270 in comparison to MTAPWT cells. Additionally, dual-drug therapies involving MTA and AG-270 result in additive effect on MTAPnull cells and antagonistic effect on MTAPWT cells. De novo purine synthesis inhibitor and drugs targeting the RAS/MAPK pathways also exhibited cell growth inhibition of MTAPnull cells. Overall, metabolic targeting of HGGs bearing CDKN2A/MTAP loss is indispensable for targeted therapy and for minimizing toxicity towards surrounding normal cells lacking similar mutations.
HGG-26. GENOMIC AND IMMUNE ANALYSIS OF PRIMARY REPLICATION-REPAIR DEFICIENT (RRD) GLIOMAS REVEALS THREE SUBGROUPS WITH DISTINCT DRIVERS AND RESPONSE TO IMMUNOTHERAPY: AN IRRDC REPORT
Authors: Nicholas R Fernandez, Anirban Das, Adrian Levine, Logine Negm, Liana Nobre, Vanessa Bianchi, Lucie Stengs, Jiil Chung, Nuno M Nunes, Melissa Edwards, Eric Bouffet, Cynthia Hawkins, Uri Tabori
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Replication-repair deficiency (RRD) caused by germline/somatic defects in mismatch repair (MMRD) and/or polymerase-proofreading genes (PPD) drives 5-10% of gliomas in children, adolescents, and young adults (CAYA). Although RRD-gliomas harbour high mutation-burden (TMB), the basis of their heterogenous biology, clinical behavior, and response to immune-checkpoint inhibitors (ICI) is unknown. METHODS We analyzed the genome (whole exome, low-coverage genome), methylome, transcriptome (bulk, single-nuclei), and the immune-microenvironment of RRD-gliomas in a large cohort of IRRDC patients and correlated these with clinical outcomes and response to ICI. RESULTS Gliomas in 202 CAYA-patients uniformly harbored hypermutation and genomic microsatellite-instability. Median TMB was 297-mutations/megabase, with frequent mutations in TP53 (90%), ATRX (85%), RAS/MAPK (80%) and IDH1/2 (15%). MMRD (but not PPD) mutational signatures contributed to the enrichment of driver mutations in POLE, IDH1, and TP53 while common pediatric mutations (K27M, G34R/V and BRAF;p.V600E) not driven by MMRD signatures were absent. Paired analyses suggested acquisition of novel variants driven by the mutational signatures that also impacted the immune microenvironment. Multi-omic analyses classified RRD-gliomas into three subgroups: RRD1 (MMRD+PPD; 60%), RRD2 (MMRD-only; 23%), and RRD3 (MMRD+IDH1/2; 16%). All RRD1-gliomas were glioblastomas with earlier age of onset, enrichment in CMMRD, arose at diverse locations including the posterior-fossa, classified in proximity to methylation-RTK1-subclass, exhibited balanced copy number profiles, harbored the highest TMB (median: 409-mutations/megabase), and immunogenic PPD signatures. Conversely, RRD3-gliomas were frequent in Lynch syndrome, presented at an older age, with predominant localization in the forebrain, more complex genomic instability, clustered in proximity to IDH1-gliomas, and harbored lower TMB (median: 33-mutations/megabase). RRD1-gliomas revealed the highest immune infiltrates with significantly improved median post-ICI survival of 52-months versus &amp;lt;12-months for RRD2/3 (p&amp;lt;0.0001). CONCLUSIONS The distinct genomic subgroups of RRD-gliomas can explain their diverse clinical outcomes, highlighting the need for developing subgroup-specific, immune-directed treatment approaches for these patients.
Laboratory Selection in Germline Genetic Testing: Laboratory Science Matters
Authors: Suzanne M. Mahon
Journal: Journal of the National Comprehensive Cancer Network (2023)

There are multiple laboratories that offer germline genetic testing, and it can be difficult to discern which one to use for testing. Some laboratories have more comprehensive analysis techniques and capability, which increases the accuracy of testing. The ordering provider has a responsibility to select the appropriate laboratory with technologic capability for the needed testing, inform the laboratory of prior testing results in the patient and family so known familial variants have targeted testing, and use appropriate terminology and nomenclature when communicating information to other healthcare professionals, patients, and families. This report presents a case illustrating the potential errors that can occur when a provider selects a laboratory that lacks the capacity to detect certain pathogenic variants, such as large deletions and duplications. False-negative germline testing results lead to missed opportunities in prevention and early detection for not only the patient but often multiple family members, which may lead to psychosocial distress and late-detected cancers. This case highlights the complexities of genetic care and why management by a genetics professional can facilitate more fiscally responsible care, appropriate genetic testing, and comprehensive care for all family members at risk.
DIPG-23. THE ROLE OF FOXO3 IN DMG RESISTANCE AND RESPONSE TO THERAPIES TARGETING DMG METABOLISM
Authors: Antonela Petrovic, Solène Fernandez, Nora Maria Uhr, Sandra Laternser, Sabine Müller, Javad Nazarian
Journal: Neuro-Oncology (2023)

Abstract Pediatric diffuse midline gliomas (DMGs), including diffuse intrinsic pontine glioma (DIPG), are the most difficult childhood brain cancers to treat, with an overall survival rate of less than 12 months from diagnosis. Despite the H3K27M mutation being the main tumor driver, activation of the PI3K/Akt pathway also occurs, altering cancer cell metabolism, increasing glycolysis, and proliferation. Our research aims to understand the underlying mechanisms of resistance to therapies targeting DMG metabolism and to develop more effective treatment strategies. We have studied the effectiveness of ONC201 in targeting DMG cancer metabolism through mitochondrial degradation, reactive oxygen species increase, and oxidative phosphorylation impairment. Our findings suggest that despite promising results in patients, DMG tumor cells switch to glycolysis after treatment through PI3K/Akt pathway activation, which contributes to chemoresistance. We have found that the FOXO3 transcription factor plays a crucial role in determining DMG tumor sensitivity to therapy, specifically in the response to combined ONC201 and PI3K inhibitors. We have shown that FOXO3 activity is abolished via PI3K pathway activation in resistant DMG cell lines, leading to cytoplasmic translocation and tumor cell survival. Additionally, we found that the expression of FOXO3 is dysregulated in DMG patient tumors. Our data implies that a failure of FOXO3 to reach the nucleus may be a contributing factor to the inadequate response seen in certain ONC201 treated DMG patients. By utilizing CRISPR-modified patient-derived DIPG cells in vitro, we investigated the impact of FOXO3 knockout/overexpression on tumor sensitivity to various treatment regimens. We have validated new PI3K inhibitors and FOXO3 activators as potential therapeutic strategies for DMG patients. Our findings suggest that targeting FOXO family of transcription factors may be a promising approach to improve the efficacy of metabolic-targeting therapies for DMGs and ultimately improve the survival of patients diagnosed with this challenging pediatric brain cancer.
ATRT-08. THE SINGLE-CELL LANDSCAPE OF PINEOBLASTOMA IDENTIFIES DEVELOPMENTAL ORIGINS AND EXPOSES TUMORIGENIC DEPENDENCIES
Authors: Brian Gudenas, Bernhard Englinger, Anthony P Y Liu, Sheikh Tanveer Ahmad, David Meredith, Elke Pfaff, Leena Paul, Jennifer Hadley, Melissa Batts, Paul Klimo Jr., Frederick A Boop, Amar Gajjar, Giles W Robinson, Brent A Orr, Hong Lin, Sanda Alexandrescu, David T W Jones, Mariella G Filbin, Paul A Northcott
Journal: Neuro-Oncology (2023)

Abstract Pineoblastoma (PB), a rare and aggressive brain tumor affecting children, presents with a highly variable age distribution and treatment outcome. Our recent bulk tumor analyses of DNA methylation and mutational landscapes uncovered four discrete PB molecular subgroups (PB-miRNA1, PB-miRNA2, PB-MYC/FOXR2, and PB-RB), providing a major advance in our understanding of biological and clinical heterogeneity. However, developmental origins of PB subgroup heterogeneity and mechanisms governing how specific genetic alterations promote malignancy remain unknown. We conducted single-nucleus RNA sequencing of 38 primary tumors, including cases from all subgroups, to uncover intra-tumoral heterogeneity, developmental origins and expose selective dependencies. Transcriptional programs driving intra-tumoral heterogeneity showed subgroup-specific patterns such as mRNA splicing associated with PB-miRNA1/2 and phototransduction in PB-RB and PB-MYC/FOXR2. Next, we created a single-cell transcriptional atlas of the murine pineal gland across 11 developmental stages and found significant associations between PB subgroups and specific differentiation states of the pinealocyte lineage, suggesting subgroup-specific developmental origins. Characterization of pineal development informed generation of biologically faithful disease models, including a novel genetically engineered mouse model of the PB-RB subgroup. PB-Rb1 mouse tumors were histologically and molecularly validated for their fidelity to human tumor counterparts, exhibiting up-regulation of key pinealocyte lineage markers that are diagnostic in patients. Using cell lines derived from our PB-Rb1 mouse model we identified several transcription factor dependencies we believe are high-jacked during normal pinealocyte development. Our findings inform the developmental origins of pineoblastoma as well as provides candidates for potential therapeutic targets.
Integrative analysis of risk factors for immune-related adverse events of checkpoint blockade therapy in cancer
Authors: Changhwan Sung, Jinhyeon An, Soohyeon Lee, Jaesoon Park, Kang Seon Lee, Il-Hwan Kim, Ji-Youn Han, Yeon Hee Park, Jee Hyun Kim, Eun Joo Kang, Min Hee Hong, Tae-Yong Kim, Jae Cheol Lee, Jae Lyun Lee, Shinkyo Yoon, Chang-Min Choi, Dae Ho Lee, Changhoon Yoo, Sang-We Kim, Jae Ho Jeong, Seyoung Seo, Sun Young Kim, Sun-Young Kong, Jung Kyoon Choi, Sook Ryun Park
Journal: Nature Cancer (2023)
MDB-28. DEEP LEARNING-BASED PERSONALIZED SURVIVAL PREDICTION FOR MEDULLOBLASTOMA
Authors: Sabina Stefan, Paul Northcott, Volker Hovestadt
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma is one of the most common malignant brain tumors in children and a leading cause of cancer-related death in this age group (5-year survival rate of ~70%). However, survival outcomes are heterogeneous, and currently associated with only a small number of clinical and molecular parameters. Instead, in this work we aim at exploiting the wealth of hidden information in genome-wide DNA methylation array data to predict accurate personalized survival probability curves for Group 3 and 4 medulloblastoma patients, the subgroups associated with the most heterogeneous outcomes. To accomplish this, we implemented a sparse neural network trained on DNA methylation and copy-number variation (CNV) profiles of over 900 medulloblastoma patients. Our network is designed specifically to leverage censored data for training, and makes no assumptions about the underlying distribution of the output survival probability curves. Furthermore, the architecture of our network is biologically interpretable, enabling us to probe the underlying biology driving survival. Our results demonstrate excellent discrimination and calibration, with a 5-year AUROC of 0.8. We compare our results to currently used stratification schemes on validation cohorts, including SJMB03 clinical trial data, and demonstrate significantly improved risk stratification (c-index of 0.66 vs 0.74, p &amp;lt; 0.0001). We find several cases in which patients assumed to be low-risk were predicted to progress rapidly, and vice versa, motivating possible refinement of risk categories in clinical practice. Our approach, which is based entirely on DNA methylation array data, may facilitate the de-escalation of therapy for low-risk patients to minimize treatment-related side effects and the intensification of treatment for high-risk individuals. The approach can be extended to other cancer types, and highlights the value of AI in healthcare towards realizing the goal of personalized medicine.
DIPG-40. HYPOXIC STRESS EXPOSES EPIGENETIC TARGETS TO ENHANCE RADIOTHERAPY RESPONSE IN H3K27M-POSITIVE PEDIATRIC DIFFUSE MIDLINE GLIOMAS
Authors: Amanda Pereira de Freitas, Monika Dzwigonska, Joanna Trubicka, Wieslawa Grajkowska, Jakub Mieczkowski, Bozena Kaminska, Katarzyna Leszczynska
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline gliomas (DMGs) are the most challenging to treat pediatric high-grade gliomas, with a dismal prognosis of 9 to 15 months of median survival. The ones localized in the pons are not accessible to the surgery and rely on radiotherapy treatment. The majority of DMGs confer a mutation in histone 3 variants (H3.3 or H3.1), leading to lysine 27 to methionine substitution (H3K27M) and a consequent global decrease in H3K27 trimethylation (H3K27me3), increased H3K27 acetylation (H3K27ac) and oncogenic changes in gene expression. An intrinsic feature of solid tumors, including DMGs, is the occurrence of hypoxic (low oxygenated) regions, which interferes with the efficiency of radiotherapy. Identifying the vulnerabilities of hypoxia-exposed tumor cells might bring new approaches in radiosensitizing DMG tumors. Hypoxia increases histone methylation in multiple solid tumors but the consequences of hypoxia-induced histone hypermethylation in H3K27M bearing tumors are unknown. Using syngeneic patient-derived DMG cell lines, we show that the presence of H3K27M prevents the hypoxia-induced hypermethylation of H3K27me3, but also impairs the hypoacetylation of histones H3 and H4 normally caused by hypoxic stress. We show that enhancing histone acetylation in hypoxic conditions with histone deacetylase (HDAC) inhibitors has a stronger sensitization effect in cells expressing H3K27M than in H3 wild-type cells. While HDAC inhibitors have been shown problematic in pediatric DMGs due to high systemic toxicity, our data points out that HDAC inhibition in the context of hypoxia may improve the therapeutic efficacy. Recent studies showed the possibility of targeting hypoxic cells with hypoxia-activated pro-drugs, including hypoxia-activated panobinostat. Our data support that such approach might be an option to target DMGs and eliminate the radiotherapy-resistant hypoxic tumor fraction, while minimizing the systemic toxicity caused by all-time active HDAC inhibitors. Studies were supported by the grant UMO-2019/33/B/NZ1/01556 (KL) from National Science Center (Poland).